The search for genetic functional variants of feed efficiency in Nelore cattle [thesis]

Gabriela Ribeiro
Identifying and selecting animals for feed efficiency (FE) is extremely important for the beef production chain. Currently, the most common parameter to access the FE animals is residual feed intake (RFI), which is the residual of the linear regression that estimates DMI based on average daily gain and mid-test metabolic body weight. However, it relies on costly and time-consuming data collection, creating a growing demand for alternative approaches to identify genetically superior animals for
more » ... E. This study aimed to detect potential liver-specific functional variants from RNA-seq data of 16 Nellore bulls (Bos indicus) divergently selected for FE. The variant call analysis detected 247 missense SNPs and nine insertion-deletions (INDELs) that alter the protein functions. These variants were found within 190 genes differentially found (P < 0.05) in liver tissue between high FE (HFE) and low FE (LFE) animals. To better understand the role of these variants in biological pathways, we performed a functional enrichment analysis, which highlighted six genes involved in complement cascade and cascade complement regulation pathways, and 20 genes involved in the regulation of the innate immune system. They had four different significant variants in the complement factor H (CFH) 21 family genes, and all were homozygous in HFE animals rather than some degree of heterozygous in LFE animals. We developed a pipeline to detect potential liver-specific functional variants from RNA-seq data from animals divergently selected for feed efficiency. With this approach, we found potential functional variants in innate immune response genes associated with feed efficiency in beef cattle.
doi:10.11606/d.74.2021.tde-02082021-125049 fatcat:kxbotxeh7rd3nmu7dr4tx7r2ai